non-target RNA-Seq in K562

	BGKLV25-1	BGKLV25-2
idx	402	403
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV25-1	BGKLV25-2
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3641	0
WB_result		4964.4
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	461	462

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV25-1	BGKLV25-1	BGKLV25-2	BGKLV25-2
Sample_ID	BGKLV25-1	BGKLV25-1	BGKLV25-2	BGKLV25-2
Sample Name	NT_BGKLV25-1	NT_BGKLV25-1B	NT_BGKLV25-2	NT_BGKLV25-2B
Sample Name	NT_BGKLV25-1	NT_BGKLV25-1B	NT_BGKLV25-2	NT_BGKLV25-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	Released	Released	Released
Status_date	2015-12-08	2016-09-24	2015-12-08	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	920	1201	921	1202

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-1	BGKLV25-1	BGKLV25-2	BGKLV25-2
Sample #
Sample Name	NT-BGKLV25-1	NT-BGKLV25-1B	NT-BGKLV25-2	NT-BGKLV25-2B
Sample_Name_Alias	NT_BGKLV25-1	NT_BGKLV25-1B	NT_BGKLV25-2	NT_BGKLV25-2B
Index Well Position	S09	S01	S10	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2016-03-04	2015-06-23	2016-03-04
Lib_ID	Lib-150623	Lib-160304	Lib-150623	Lib-160304
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/B1.png	DNA_Library_LV33-34-25B-32/set1/A5.png	DNA_Library_LV24-25-26/set1/C1.png	DNA_Library_LV33-34-25B-32/set1/B5.png
RIN	10.0	10.0	9.9	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A9.png	RNA_Library_LV22-23-25/set1/A9.png	RNA_Library_LV22-23-25/set1/B9.png	RNA_Library_LV22-23-25/set1/B9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-1	BGKLV25-1	BGKLV25-2	BGKLV25-2
RBP	NT	NT	NT	NT
Batch_ID	BGKLV25	BGKLV25	BGKLV25	BGKLV25
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2612	2900	2613	2901

Sequencing Information

	BGKLV25-1	BGKLV25-1	BGKLV25-2	BGKLV25-2
Sample_ID	BGKLV25-1	BGKLV25-1	BGKLV25-2	BGKLV25-2
Sample Name	NT_BGKLV25-1	NT_BGKLV25-1B	NT_BGKLV25-2	NT_BGKLV25-2B
Pool ID	Pool-151101	Pool-160425	Pool-151101	Pool-160425
LocalServer_folder	set25	set25	set25	set25
total_reads	67,425,006	103,914,872	160,852,324	99,221,152
total_aligned_reads	67,692,652	77,978,392	163,203,564	75,780,896
unique_aligned_reads	62,015,428	71,090,814	148,536,488	69,192,056
percent_uniqueAligned	0.91977	0.68413	0.92343	0.69735
correlation_replicates	0.997955	0.998179	0.997955	0.998179
spikein_reads	333,084	381,950	812,252	385,444
percent_spikeins	0.00494	0.00368	0.00505	0.00388
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1254	1549	1255	1550

Data Submission Information

	BGKLV25-1	BGKLV25-1
ENCODE_alias	brenton-graveley:NT_BGKLV25	brenton-graveley:NT_BGKLV25B
ENCODE_accession	ENCSR620PUP	ENCSR031RRO
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-1	BGKLV25-1
Sample Name	NT_BGKLV25-1	NT_BGKLV25-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2016-05-25
Project	ENCODE3	ENCODE3

protocol_URL
ID	3009	3140

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	Project	FILE_ID
NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1549	HiSeq2000	100	paired-ended	1				ENCODE3	19580
NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1254	HiSeq2000	100	paired-ended	1				ENCODE3	19581
NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1549	HiSeq2000	100	paired-ended	2				ENCODE3	19616
NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1254	HiSeq2000	100	paired-ended	2				ENCODE3	19617
NT_BGKLV25-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1549					GRCh38	V40	NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz	ENCORE2	19652
NT_BGKLV25-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1254					GRCh38	V40	NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz	ENCORE2	19653
NT_BGKLV25-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1549					GRCh38	V40	NT_BGKLV25-1B/Aligned.sortedByCoord.out.bam	ENCORE2	19688
NT_BGKLV25-1_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1254					GRCh38	V40	NT_BGKLV25-1/Aligned.sortedByCoord.out.bam	ENCORE2	19689
NT_BGKLV25-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1549					GRCh38	V40	NT_BGKLV25-1B/Aligned.sortedByCoord.out.bam	ENCORE2	19724
NT_BGKLV25-1_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1254					GRCh38	V40	NT_BGKLV25-1/Aligned.sortedByCoord.out.bam	ENCORE2	19725
NT_BGKLV25-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1549					GRCh38	V40	NT_BGKLV25-1B/Aligned.sortedByCoord.out.bam	ENCORE2	19760
NT_BGKLV25-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1254					GRCh38	V40	NT_BGKLV25-1/Aligned.sortedByCoord.out.bam	ENCORE2	19761
NT_BGKLV25-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1549					GRCh38	V40	NT_BGKLV25-1B/Aligned.sortedByCoord.out.bam	ENCORE2	19796
NT_BGKLV25-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1254					GRCh38	V40	NT_BGKLV25-1/Aligned.sortedByCoord.out.bam	ENCORE2	19797
NT_BGKLV25-1B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1549					GRCh38	V40	NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz	ENCORE2	19986
NT_BGKLV25-1_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1254					GRCh38	V40	NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz	ENCORE2	19987
NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1550	HiSeq2000	100	paired-ended	1				ENCODE3	19582
NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1255	HiSeq2000	100	paired-ended	1				ENCODE3	19583
NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1550	HiSeq2000	100	paired-ended	2				ENCODE3	19618
NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1255	HiSeq2000	100	paired-ended	2				ENCODE3	19619
NT_BGKLV25-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1550					GRCh38	V40	NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCORE2	19654
NT_BGKLV25-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1255					GRCh38	V40	NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCORE2	19655
NT_BGKLV25-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1550					GRCh38	V40	NT_BGKLV25-2B/Aligned.sortedByCoord.out.bam	ENCORE2	19690
NT_BGKLV25-2_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1255					GRCh38	V40	NT_BGKLV25-2/Aligned.sortedByCoord.out.bam	ENCORE2	19691
NT_BGKLV25-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1550					GRCh38	V40	NT_BGKLV25-2B/Aligned.sortedByCoord.out.bam	ENCORE2	19726
NT_BGKLV25-2_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1255					GRCh38	V40	NT_BGKLV25-2/Aligned.sortedByCoord.out.bam	ENCORE2	19727
NT_BGKLV25-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1550					GRCh38	V40	NT_BGKLV25-2B/Aligned.sortedByCoord.out.bam	ENCORE2	19762
NT_BGKLV25-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1255					GRCh38	V40	NT_BGKLV25-2/Aligned.sortedByCoord.out.bam	ENCORE2	19763
NT_BGKLV25-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1550					GRCh38	V40	NT_BGKLV25-2B/Aligned.sortedByCoord.out.bam	ENCORE2	19798
NT_BGKLV25-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1255					GRCh38	V40	NT_BGKLV25-2/Aligned.sortedByCoord.out.bam	ENCORE2	19799
NT_BGKLV25-2B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1550					GRCh38	V40	NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCORE2	19988
NT_BGKLV25-2_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1255					GRCh38	V40	NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCORE2	19989